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This page was generated on 2025-09-25 11:42 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 999/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTSeqGenie 4.38.0  (landing page)
Jens Reeder
Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/HTSeqGenie
git_branch: RELEASE_3_21
git_last_commit: 1638d9f
git_last_commit_date: 2025-04-15 10:16:04 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
merida1macOS 12.7.5 Monterey / x86_64... NOT SUPPORTED ...
kjohnson1macOS 13.6.6 Ventura / arm64... NOT SUPPORTED ...
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  

CHECK results for HTSeqGenie on kunpeng2

To the developers/maintainers of the HTSeqGenie package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HTSeqGenie.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: HTSeqGenie
Version: 4.38.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.38.0.tar.gz
StartedAt: 2025-09-23 10:53:44 -0000 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 11:33:44 -0000 (Tue, 23 Sep 2025)
EllapsedTime: 2400.5 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: HTSeqGenie.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HTSeqGenie.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.38.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTSeqGenie’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘ShortRead:::.set_omp_threads’ ‘gmapR:::..gsnap’ ‘gmapR:::GeneGenome’
  ‘gmapR:::checkPackageInstalled’ ‘gmapR:::getDefaultGmapGenomePath’
  ‘gmapR:::getGeneRoi’ ‘gmapR:::subsetRegion’ ‘parallel:::mckill’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.makePreprocessAlignPlots: no visible binding for global variable
  ‘data’
.plot.in.out.min.max.readlength: no visible global function definition
  for ‘median’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.lfqs’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.chunkid’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.subsampling_filter’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.max_nbchunks’
addHandler: no visible binding for '<<-' assignment to
  ‘logging.handlers’
addHandler: no visible binding for global variable ‘logging.handlers’
addHandler: no visible binding for '<<-' assignment to ‘logging.file’
buildAnyFastaGenome: no visible global function definition for ‘getSeq’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘gaps’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘ranges’
buildTP53FastaGenome: no visible global function definition for
  ‘getSeq’
buildTallyParam: no visible global function definition for ‘seqinfo’
computeCoverage: no visible global function definition for ‘resize’
computeCoverage: no visible global function definition for ‘coverage’
estimateCutoffs : <anonymous>: no visible binding for global variable
  ‘quantile’
getGenomeSegments: no visible global function definition for ‘seqinfo’
hashVariants: no visible global function definition for ‘ranges’
isAboveQualityThresh: no visible global function definition for ‘Views’
isAboveQualityThresh: no visible global function definition for
  ‘viewMeans’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.n’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.x’
logReset: no visible binding for '<<-' assignment to ‘logging.handlers’
logReset: no visible binding for '<<-' assignment to ‘logging.loglevel’
logReset: no visible binding for '<<-' assignment to ‘logging.file’
loglevel: no visible binding for global variable ‘logging.loglevel’
loglevel: no visible binding for global variable ‘logging.handlers’
processChunks : tracefun: no visible binding for global variable
  ‘sjobs’
processChunks : tracefun: no visible binding for global variable
  ‘chunkid’
setLevel: no visible binding for '<<-' assignment to ‘logging.loglevel’
statCountFeatures: no visible global function definition for ‘quantile’
truncateReads: no visible global function definition for ‘subseq’
vcfStat: no visible global function definition for ‘quantile’
writeToFile: no visible binding for global variable ‘logging.file’
Undefined global functions or variables:
  Views chunkid coverage data gaps getSeq logging.file logging.handlers
  logging.loglevel median quantile ranges resize seqinfo sjobs subseq
  viewMeans
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) calculateTargetLengths.Rd:17: Lost braces; missing escapes or markup?
    17 | Target length table and writes two files in {save_dir}/reports/images/TargetLenghts.[pdf|png]"
       |                                             ^
checkRd: (-1) initLog.Rd:18: Lost braces; missing escapes or markup?
    18 | Setup logging file in {save_dir}/progress.log
       |                       ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'findVariantFile.Rd':
  ‘dir_path’

Documented arguments not in \usage in Rd file 'logdebug.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'logerror.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'loginfo.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'logwarn.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’

Installation output

HTSeqGenie.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** this is package ‘HTSeqGenie’ version ‘4.38.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

Tests output

HTSeqGenie.Rcheck/tests/doRUnit.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("HTSeqGenie")
Loading required package: gmapR
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: VariantAnnotation

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Warning message:
In fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
> 
> source(getPackageFile("unitTests/runTests.R"))
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
did not source anything in dirname= ./R 


Executing test function test.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:01:11.689226 INFO::preprocessReads.R/preprocessReads: starting...
2025-09-23 11:01:11.698339 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:01:11.703997 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-09-23 11:01:11.706846 DEBUG::tools.R/processChunks: starting...
2025-09-23 11:01:14.957064 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-09-23 11:01:14.959073 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/chunks/chunk_000001/logs/progress.log
2025-09-23 11:01:17.879157 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes
2025-09-23 11:01:17.881009 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/chunks/chunk_000002/logs/progress.log
2025-09-23 11:01:20.766808 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2025-09-23 11:01:20.768774 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/chunks/chunk_000003/logs/progress.log
2025-09-23 11:01:23.683703 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2025-09-23 11:01:23.722849 DEBUG::tools.R/processChunks: done
2025-09-23 11:01:23.727704 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-09-23 11:01:23.730934 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/results/test_pe.adapter_contaminated_1.RData
2025-09-23 11:01:23.734881 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-09-23 11:01:23.737463 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/results/test_pe.adapter_contaminated_2.RData
2025-09-23 11:01:23.749575 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-09-23 11:01:23.752664 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/results/test_pe.summary_preprocess.tab
2025-09-23 11:01:23.757 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/bams/processed.aligner_input_1.fastq ...
2025-09-23 11:01:23.763332 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/bams/processed.aligner_input_2.fastq ...
2025-09-23 11:01:23.768611 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/reports/shortReadReport_1 ...
2025-09-23 11:01:25.650964 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/reports/shortReadReport_2 ...
2025-09-23 11:01:28.745813 INFO::preprocessReads.R/preprocessReads: done
2025-09-23 11:01:28.808792 INFO::alignReads.R/alignReads: starting alignment...
2025-09-23 11:01:28.814726 DEBUG::tools.R/processChunks: starting...
2025-09-23 11:01:32.18092 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-09-23 11:01:32.183222 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/chunks/chunk_000001/logs/progress.log
2025-09-23 11:01:35.360415 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.053 minutes
2025-09-23 11:01:35.362662 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-09-23 11:01:38.117999 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-09-23 11:01:38.120334 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-09-23 11:01:40.869615 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-09-23 11:01:40.877148 DEBUG::tools.R/processChunks: done
2025-09-23 11:01:40.879165 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-09-23 11:01:41.200128 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-09-23 11:01:41.211446 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/results/test_pe.summary_alignment.tab
2025-09-23 11:01:41.222321 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/results/test_pe.summary_analyzed_bamstats.tab
2025-09-23 11:01:41.224788 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-09-23 11:01:41.503759 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.2de16c6890142/results/test_pe.summary_target_lengths.tab
2025-09-23 11:01:41.564608 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-09-23 11:01:41.565892 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:01:41.848198 INFO::preprocessReads.R/preprocessReads: starting...
2025-09-23 11:01:41.851632 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:01:41.927774 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-09-23 11:01:41.933885 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:01:41.938082 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-09-23 11:01:41.940623 DEBUG::tools.R/processChunks: starting...
2025-09-23 11:01:45.4363 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-09-23 11:01:45.438307 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.sparsechunks.2de16c3a552f73/chunks/chunk_000001/logs/progress.log
2025-09-23 11:01:48.297308 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-09-23 11:01:48.299275 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.sparsechunks.2de16c3a552f73/chunks/chunk_000002/logs/progress.log
2025-09-23 11:01:51.097352 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-09-23 11:01:51.099315 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.sparsechunks.2de16c3a552f73/chunks/chunk_000003/logs/progress.log
2025-09-23 11:01:54.04668 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2025-09-23 11:01:54.048782 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.sparsechunks.2de16c3a552f73/chunks/chunk_000004/logs/progress.log
2025-09-23 11:01:56.861822 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.047 minutes
2025-09-23 11:01:56.91928 DEBUG::tools.R/processChunks: done
2025-09-23 11:01:56.927493 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-09-23 11:01:56.930855 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.sparsechunks.2de16c3a552f73/results/test_pe.adapter_contaminated_1.RData
2025-09-23 11:01:56.935077 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-09-23 11:01:56.937715 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.sparsechunks.2de16c3a552f73/results/test_pe.adapter_contaminated_2.RData
2025-09-23 11:01:56.951612 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2 highqual_reads=1 adapter_contam=0 read_length=75 rRNA_contam_reads=0 processed_reads=1 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-09-23 11:01:56.954689 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.sparsechunks.2de16c3a552f73/results/test_pe.summary_preprocess.tab
2025-09-23 11:01:56.95942 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.sparsechunks.2de16c3a552f73/bams/processed.aligner_input_1.fastq ...
2025-09-23 11:01:56.966053 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.sparsechunks.2de16c3a552f73/bams/processed.aligner_input_2.fastq ...
2025-09-23 11:01:56.971311 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.sparsechunks.2de16c3a552f73/reports/shortReadReport_1 ...
2025-09-23 11:01:58.795793 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReads.sparsechunks.2de16c3a552f73/reports/shortReadReport_2 ...
2025-09-23 11:02:01.880768 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:02:02.094501 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-09-23 11:02:02.101355 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -D /home/biocbuild/.local/share/gmap -t 1 -d TP53_demo_3.2.2 --quality-protocol=illumina  -A sam --read-group-id=test_se -m 0 --split-output /home/biocbuild/tmp/RtmpDgxaoT/test.alignReadsOneSingleEnd.2de16c1ce4fee7/bams/test.alignReads /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-09-23 11:02:02.259852 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-09-23 11:02:02.388881 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReadsOneSingleEnd.2de16c1ce4fee7/results/test.alignReads.summary_alignment.tab
2025-09-23 11:02:02.445959 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.alignReadsOneSingleEnd.2de16c1ce4fee7/results/test.alignReads.summary_analyzed_bamstats.tab
2025-09-23 11:02:02.447998 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.003 0 0.004
Error in DEACTIVATED("Skipped annotateVariants() test") : 
  Skipped annotateVariants() test
In addition: There were 11 warnings (use warnings() to see them)
 done successfully.



Executing test function test.callVariantsVariantTools.genotype  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:02:02.843892 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.genotype.2de16c43b88dc5/results/test_pe.coverage.RData
2025-09-23 11:02:02.846354 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.genotype.2de16c43b88dc5/results/test_pe.coverage.bw
2025-09-23 11:02:03.02553 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.genotype.2de16c43b88dc5/results/test_pe.summary_coverage.tab
2025-09-23 11:02:03.02787 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-09-23 11:02:14.66815 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-09-23 11:02:14.800235 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-09-23 11:02:14.826897 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-09-23 11:02:14.829148 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.genotype.2de16c43b88dc5/results/test_pe.raw_variants.RData
2025-09-23 11:02:14.832428 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.genotype.2de16c43b88dc5/results/test_pe.filtered_variants.RData
2025-09-23 11:02:14.834615 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-09-23 11:02:14.836431 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-09-23 11:02:15.445182 INFO::analyzeVariants.R/writeVCF: ...done
2025-09-23 11:02:15.446901 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-09-23 11:03:42.860857 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-09-23 11:03:43.493372 INFO::analyzeVariants.R/writeVCF: ...done
2025-09-23 11:03:43.494607 INFO::analyzeVariants.R/.callGenotypes: done
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
 done successfully.



Executing test function test.wrap.callVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:03:44.060325 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-09-23 11:03:55.789601 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-09-23 11:03:55.904274 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-09-23 11:03:55.928958 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-09-23 11:03:55.930914 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.wrap.callVariants.2de16c4bd5e4c0/results/test_pe.raw_variants.RData
2025-09-23 11:03:55.934007 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.wrap.callVariants.2de16c4bd5e4c0/results/test_pe.filtered_variants.RData
2025-09-23 11:03:55.935869 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.filters  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:03:56.125905 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-09-23 11:04:07.427678 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-09-23 11:04:07.513507 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-09-23 11:04:07.538284 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-09-23 11:04:07.540222 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.wrap.callVariants.filters.2de16c6735fc3d/results/test_pe.raw_variants.RData
2025-09-23 11:04:07.543298 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.wrap.callVariants.filters.2de16c6735fc3d/results/test_pe.filtered_variants.RData
2025-09-23 11:04:07.545046 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-09-23 11:04:07.54697 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-09-23 11:04:18.89969 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-09-23 11:04:18.956937 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-09-23 11:04:18.982512 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-09-23 11:04:18.9845 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.wrap.callVariants.filters.2de16c6735fc3d/results/test_pe.raw_variants.RData
2025-09-23 11:04:18.987948 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.wrap.callVariants.filters.2de16c6735fc3d/results/test_pe.filtered_variants.RData
2025-09-23 11:04:18.990725 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.which  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:04:19.311136 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-09-23 11:04:19.313152 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-09-23 11:04:22.892953 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-09-23 11:04:23.025422 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-09-23 11:04:23.052772 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-09-23 11:04:23.055052 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.wrap.callVariants.which.2de16c563c542/results/test_pe.raw_variants.RData
2025-09-23 11:04:23.057958 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.wrap.callVariants.which.2de16c563c542/results/test_pe.filtered_variants.RData
2025-09-23 11:04:23.06022 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:04:23.267066 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-09-23 11:04:23.269018 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:04:23.511032 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-09-23 11:04:23.864448 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.isFirstFragment  ...  done successfully.



Executing test function test.buildCountsGRangesList  ...   403 genes were dropped because they have exons located on both strands of the
  same reference sequence or on more than one reference sequence, so cannot be
  represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
  object, or use suppressMessages() to suppress this message.
 done successfully.



Executing test function test.generateSingleGeneDERs  ...  done successfully.



Executing test function test.computeCoverage  ...  done successfully.



Executing test function test.isSparse  ...  done successfully.



Executing test function test.mergeCoverage  ... 2025-09-23 11:05:37.52638 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/gqalmsyf/merged/results/bla.coverage.RData
2025-09-23 11:05:37.529567 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpDgxaoT/gqalmsyf/merged/results/bla.coverage.bw
2025-09-23 11:05:37.643596 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/gqalmsyf/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-09-23 11:05:39.038095 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/ywkzaeif/merged/results/bla.coverage.RData
2025-09-23 11:05:39.040231 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpDgxaoT/ywkzaeif/merged/results/bla.coverage.bw
2025-09-23 11:05:39.05484 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/ywkzaeif/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.findTemplate  ...  done successfully.



Executing test function test.checkConfig  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.checkConfig.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.getConfig  ...  done successfully.



Executing test function test.loadConfig  ...  done successfully.



Executing test function test.parseDCF  ...  done successfully.



Executing test function test.updateConfig  ...  done successfully.



Executing test function test.getAdapterSeqs  ...  done successfully.



Executing test function test.isAdapter  ...  done successfully.



Executing test function test.isAdapter3.primeEnd  ...  done successfully.



Executing test function test.detectRRNA  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:05:40.758882 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-09-23 11:05:40.760365 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpDgxaoT/test.detectRRNA.2de16c2b6d0e55/bams/rRNA_contam/input1.fastq
2025-09-23 11:05:40.764764 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmpDgxaoT/test.detectRRNA.2de16c2b6d0e55/bams/rRNA_contam/test_se /home/biocbuild/tmp/RtmpDgxaoT/test.detectRRNA.2de16c2b6d0e55/bams/rRNA_contam/input1.fastq 2>&1
2025-09-23 11:05:40.876392 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-09-23 11:05:40.877844 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:05:41.08304 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-09-23 11:05:41.08438 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpDgxaoT/test.detectRRNA.paired_end.2de16c6a924063/bams/rRNA_contam/input1.fastq
2025-09-23 11:05:41.086525 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpDgxaoT/test.detectRRNA.paired_end.2de16c6a924063/bams/rRNA_contam/input2.fastq
2025-09-23 11:05:41.089668 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmpDgxaoT/test.detectRRNA.paired_end.2de16c6a924063/bams/rRNA_contam/test_pe /home/biocbuild/tmp/RtmpDgxaoT/test.detectRRNA.paired_end.2de16c6a924063/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/RtmpDgxaoT/test.detectRRNA.paired_end.2de16c6a924063/bams/rRNA_contam/input2.fastq 2>&1
2025-09-23 11:05:41.348447 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-09-23 11:05:41.349937 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-09-23 11:05:41.380951 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmpDgxaoT/test_get_rRNA_idssemgcopf/test_pe /home/biocbuild/tmp/RtmpDgxaoT/test_get_rRNA_idssemgcopf/1.fastq -a paired /home/biocbuild/tmp/RtmpDgxaoT/test_get_rRNA_idssemgcopf/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-09-23 11:05:41.681429 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmpDgxaoT/test_get_rRNAIds_randombjhxqztd/test_pe /home/biocbuild/tmp/RtmpDgxaoT/test_get_rRNAIds_randombjhxqztd/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-09-23 11:05:41.858633 INFO::filterQuality.R/filterQuality: filterByLength...
2025-09-23 11:05:41.860627 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-09-23 11:05:41.861928 INFO::filterQuality.R/filterByLength: done
2025-09-23 11:05:41.931532 INFO::filterQuality.R/filterQuality: filterByLength...
2025-09-23 11:05:41.93289 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-09-23 11:05:41.934221 INFO::filterQuality.R/filterByLength: done
 done successfully.



Executing test function test.isAboveQualityThresh  ...  done successfully.



Executing test function test.trimTailsByQuality  ... 2025-09-23 11:05:42.010922 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-09-23 11:05:42.023786 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-09-23 11:05:42.025378 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-09-23 11:05:42.032064 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-09-23 11:05:42.033626 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-09-23 11:05:42.040376 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-09-23 11:05:42.042002 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-09-23 11:05:42.049079 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



Executing test function test.callVariantsGATK  ... Timing stopped at: 0 0 0.001
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") : 
  callVariantsGATK() tests need gatk.path option set
In addition: There were 50 or more warnings (use warnings() to see the first 50)
 done successfully.



Executing test function test.callVariantsGATK.withFiltering  ... Timing stopped at: 0 0 0.001
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") : 
  callVariantsGATK() tests need gatk.path option set
 done successfully.



Executing test function test.checkGATKJar  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("checkGATKJar() test needs gatk.path option set") : 
  checkGATKJar() test needs gatk.path option set
 done successfully.



Executing test function test.excludeVariantsByRegion  ...  done successfully.



Executing test function test.gatk  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("gatk() tests need gatk.path option set") : 
  gatk() tests need gatk.path option set
 done successfully.



Executing test function test.realignIndels  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("test.realignIndels() tests need gatk.path option set") : 
  test.realignIndels() tests need gatk.path option set
 done successfully.



Executing test function test.realignIndelsGATK  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("realignIndelsGATK() tests need gatk.path option set") : 
  realignIndelsGATK() tests need gatk.path option set
 done successfully.



Executing test function test.realignIndelsGATK.parallel  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("realignIndelsGATK() tests need gatk.path option set") : 
  realignIndelsGATK() tests need gatk.path option set
 done successfully.



Executing test function test_zipUp  ...  done successfully.



Executing test function test.FastQStreamer.getReads.pefq  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:05:42.47706 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:05:42.48046 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.pefq.subsample  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:05:42.735586 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:05:42.89851 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-09-23 11:05:42.902431 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:05:42.905845 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.segz  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:05:44.525434 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/reads.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.getReads.truncated  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:05:44.722603 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/truncated.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.subsampler.isdeterministic  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:05:44.948881 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:05:45.059479 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-09-23 11:05:45.063044 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:05:45.066372 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:05:45.368015 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:05:45.436853 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-09-23 11:05:45.440355 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:05:45.443753 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.createTmpDir  ...  done successfully.



Executing test function test.detectQualityInFASTQFile  ...  done successfully.



Executing test function test.getObjectFilename  ...  done successfully.



Executing test function test.safeUnlink  ...  done successfully.



Executing test function test.writeAudit  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:05:46.444372 INFO::preprocessReads.R/preprocessReads: starting...
2025-09-23 11:05:46.451697 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:05:46.456731 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-09-23 11:05:46.460221 DEBUG::tools.R/processChunks: starting...
2025-09-23 11:05:50.022635 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-09-23 11:05:50.024844 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/chunks/chunk_000001/logs/progress.log
2025-09-23 11:05:52.817684 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-09-23 11:05:52.819732 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/chunks/chunk_000002/logs/progress.log
2025-09-23 11:05:55.615555 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-09-23 11:05:55.617739 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/chunks/chunk_000003/logs/progress.log
2025-09-23 11:05:58.409871 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.047 minutes
2025-09-23 11:05:58.507329 DEBUG::tools.R/processChunks: done
2025-09-23 11:05:58.511694 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-09-23 11:05:58.514561 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.adapter_contaminated_1.RData
2025-09-23 11:05:58.518057 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-09-23 11:05:58.520828 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.adapter_contaminated_2.RData
2025-09-23 11:05:58.533827 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-09-23 11:05:58.536829 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.summary_preprocess.tab
2025-09-23 11:05:58.54075 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/bams/processed.aligner_input_1.fastq ...
2025-09-23 11:05:58.547904 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/bams/processed.aligner_input_2.fastq ...
2025-09-23 11:05:58.553898 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/reports/shortReadReport_1 ...
2025-09-23 11:06:00.589946 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/reports/shortReadReport_2 ...
2025-09-23 11:06:02.208792 INFO::preprocessReads.R/preprocessReads: done
2025-09-23 11:06:02.298639 INFO::alignReads.R/alignReads: starting alignment...
2025-09-23 11:06:02.303991 DEBUG::tools.R/processChunks: starting...
2025-09-23 11:06:05.871046 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-09-23 11:06:05.873421 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/chunks/chunk_000001/logs/progress.log
2025-09-23 11:06:08.499451 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-09-23 11:06:08.501653 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-09-23 11:06:11.219938 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-09-23 11:06:11.222398 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-09-23 11:06:13.886032 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-09-23 11:06:13.889756 DEBUG::tools.R/processChunks: done
2025-09-23 11:06:13.891847 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-09-23 11:06:14.197121 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-09-23 11:06:14.207945 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.summary_alignment.tab
2025-09-23 11:06:14.21822 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.summary_analyzed_bamstats.tab
2025-09-23 11:06:14.220886 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-09-23 11:06:14.479303 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.summary_target_lengths.tab
2025-09-23 11:06:14.54187 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-09-23 11:06:14.543279 INFO::alignReads.R/alignReads: done
2025-09-23 11:06:14.630215 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-09-23 11:06:14.651617 DEBUG::tools.R/processChunks: starting...
2025-09-23 11:06:18.104915 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-09-23 11:06:18.107075 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/chunks/chunk_000001/logs/progress.log
2025-09-23 11:06:20.687575 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-09-23 11:06:20.689885 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/chunks/chunk_000002/logs/progress.log
2025-09-23 11:06:23.282303 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-09-23 11:06:23.284338 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/chunks/chunk_000003/logs/progress.log
2025-09-23 11:06:25.871777 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-09-23 11:06:25.875141 DEBUG::tools.R/processChunks: done
2025-09-23 11:06:25.877469 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-09-23 11:06:25.894252 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.counts_exon.tab
2025-09-23 11:06:25.907669 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.counts_exon_disjoint.tab
2025-09-23 11:06:25.916455 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.counts_gene.tab
2025-09-23 11:06:25.923526 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.counts_gene_coding.tab
2025-09-23 11:06:25.930458 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.counts_gene_exonic.tab
2025-09-23 11:06:25.937477 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.counts_intergenic.tab
2025-09-23 11:06:25.949129 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.counts_intron.tab
2025-09-23 11:06:25.952792 INFO::countGenomicFeatures.R/mergeCounts: done
2025-09-23 11:06:25.960441 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.summary_counts.tab
2025-09-23 11:06:25.962745 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-09-23 11:06:26.321012 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-09-23 11:06:26.322322 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-09-23 11:06:26.463112 INFO::coverage.R/calculateCoverage: starting...
2025-09-23 11:06:26.468115 DEBUG::tools.R/processChunks: starting...
2025-09-23 11:06:30.020068 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-09-23 11:06:30.022552 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/chunks/chunk_000001/logs/progress.log
2025-09-23 11:06:32.241751 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2025-09-23 11:06:32.243974 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/chunks/chunk_000002/logs/progress.log
2025-09-23 11:06:34.470973 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2025-09-23 11:06:34.473386 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/chunks/chunk_000003/logs/progress.log
2025-09-23 11:06:36.708078 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2025-09-23 11:06:36.711661 DEBUG::tools.R/processChunks: done
2025-09-23 11:06:38.635978 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.coverage.RData
2025-09-23 11:06:38.638036 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.coverage.bw
2025-09-23 11:06:38.654878 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.summary_coverage.tab
2025-09-23 11:06:38.660591 INFO::coverage.R/calculateCoverage: done
2025-09-23 11:06:38.665369 INFO::analyzeVariants/analyzeVariants: starting ...
2025-09-23 11:06:38.766553 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-09-23 11:06:42.722706 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-09-23 11:06:42.832118 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-09-23 11:06:42.856086 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-09-23 11:06:42.858032 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.raw_variants.RData
2025-09-23 11:06:42.860323 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.filtered_variants.RData
2025-09-23 11:06:42.862123 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-09-23 11:06:42.863542 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-09-23 11:06:43.183121 INFO::analyzeVariants.R/writeVCF: ...done
2025-09-23 11:06:43.325989 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/results/test_pe.summary_variants.tab
2025-09-23 11:06:43.328957 INFO::analyzeVariants/analyzeVariants: done
2025-09-23 11:06:43.332784 INFO::Pipeline run successful.
2025-09-23 11:06:43.518373 INFO::mergeLanes.R/doMergeLanes: starting...
2025-09-23 11:06:43.52395 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-09-23 11:06:43.527048 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.adapter_contaminated_1.RData
2025-09-23 11:06:43.53097 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-09-23 11:06:43.533806 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.adapter_contaminated_2.RData
2025-09-23 11:06:43.548457 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-09-23 11:06:43.551691 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.summary_preprocess.tab
2025-09-23 11:06:43.554605 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-09-23 11:06:43.895847 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-09-23 11:06:43.905999 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.summary_alignment.tab
2025-09-23 11:06:43.917126 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.summary_analyzed_bamstats.tab
2025-09-23 11:06:43.919905 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-09-23 11:06:44.189807 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.summary_target_lengths.tab
2025-09-23 11:06:44.254597 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-09-23 11:06:44.29854 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-09-23 11:06:44.323816 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.counts_exon.tab
2025-09-23 11:06:44.339904 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.counts_exon_disjoint.tab
2025-09-23 11:06:44.349662 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.counts_gene.tab
2025-09-23 11:06:44.35786 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.counts_gene_coding.tab
2025-09-23 11:06:44.366087 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.counts_gene_exonic.tab
2025-09-23 11:06:44.374372 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.counts_intergenic.tab
2025-09-23 11:06:44.391615 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.counts_intron.tab
2025-09-23 11:06:44.395839 INFO::countGenomicFeatures.R/mergeCounts: done
2025-09-23 11:06:44.404275 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.summary_counts.tab
2025-09-23 11:06:44.40694 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-09-23 11:06:44.701122 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-09-23 11:06:47.048275 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.coverage.RData
2025-09-23 11:06:47.054822 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.coverage.bw
2025-09-23 11:06:47.070729 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.summary_coverage.tab
2025-09-23 11:06:47.109989 INFO::analyzeVariants/analyzeVariants: starting ...
2025-09-23 11:06:47.186132 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-09-23 11:06:51.024572 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-09-23 11:06:51.191054 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-09-23 11:06:51.218091 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-09-23 11:06:51.22012 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.raw_variants.RData
2025-09-23 11:06:51.222565 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.filtered_variants.RData
2025-09-23 11:06:51.22445 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-09-23 11:06:51.226038 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-09-23 11:06:51.588596 INFO::analyzeVariants.R/writeVCF: ...done
2025-09-23 11:06:51.745322 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.mergeLanes.2de16c7622cd0e/merged/results/merged.summary_variants.tab
2025-09-23 11:06:51.748225 INFO::analyzeVariants/analyzeVariants: done
2025-09-23 11:06:51.757164 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



Executing test function test.markDuplicates  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("Skipped markDuplicates() test") : 
  Skipped markDuplicates() test
In addition: There were 28 warnings (use warnings() to see them)
 done successfully.



Executing test function test.markDuplicates_w_outfile  ... Timing stopped at: 0 0 0.001
Error in DEACTIVATED("Skipped markDuplicates() test") : 
  Skipped markDuplicates() test
 done successfully.



Executing test function test.preprocessReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:06:52.157482 INFO::preprocessReads.R/preprocessReads: starting...
2025-09-23 11:06:52.182673 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:06:52.214503 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-09-23 11:06:52.218069 DEBUG::tools.R/processChunks: starting...
2025-09-23 11:06:56.030751 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-09-23 11:06:56.032966 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpDgxaoT/test.preprocessReads.2de16c4fd3ed/chunks/chunk_000001/logs/progress.log
2025-09-23 11:06:58.827363 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-09-23 11:06:58.912584 DEBUG::tools.R/processChunks: done
2025-09-23 11:06:58.915638 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-09-23 11:06:58.917962 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.preprocessReads.2de16c4fd3ed/results/test_pe.adapter_contaminated_1.RData
2025-09-23 11:06:58.9204 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-09-23 11:06:58.922558 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.preprocessReads.2de16c4fd3ed/results/test_pe.adapter_contaminated_2.RData
2025-09-23 11:06:58.931313 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-09-23 11:06:58.934195 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpDgxaoT/test.preprocessReads.2de16c4fd3ed/results/test_pe.summary_preprocess.tab
2025-09-23 11:06:58.937116 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpDgxaoT/test.preprocessReads.2de16c4fd3ed/bams/processed.aligner_input_1.fastq ...
2025-09-23 11:06:58.94276 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpDgxaoT/test.preprocessReads.2de16c4fd3ed/bams/processed.aligner_input_2.fastq ...
2025-09-23 11:06:58.948008 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpDgxaoT/test.preprocessReads.2de16c4fd3ed/reports/shortReadReport_1 ...
2025-09-23 11:07:00.879732 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpDgxaoT/test.preprocessReads.2de16c4fd3ed/reports/shortReadReport_2 ...
2025-09-23 11:07:02.363286 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpDgxaoT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-09-23 11:07:02.68751 INFO::preprocessReads.R/preprocessReads: starting...
2025-09-23 11:07:02.694347 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-09-23 11:07:02.698982 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-09-23 11:07:02.701975 DEBUG::tools.R/processChunks: starting...
2025-09-23 11:08:02.71624 DEBUG::tools.R/traceMem: wired.mem=-4.273656 GiB
2025-09-23 11:09:02.785788 DEBUG::tools.R/traceMem: wired.mem=-7.959400 GiB
2025-09-23 11:10:02.85334 DEBUG::tools.R/traceMem: wired.mem=-3.630871 GiB
2025-09-23 11:11:02.927782 DEBUG::tools.R/traceMem: wired.mem=-3.984495 GiB
2025-09-23 11:12:03.008874 DEBUG::tools.R/traceMem: wired.mem=-5.326303 GiB
2025-09-23 11:13:03.084872 DEBUG::tools.R/traceMem: wired.mem=1.683296 GiB
2025-09-23 11:14:03.160944 DEBUG::tools.R/traceMem: wired.mem=5.797442 GiB
2025-09-23 11:15:03.236852 DEBUG::tools.R/traceMem: wired.mem=6.179222 GiB
2025-09-23 11:16:03.312841 DEBUG::tools.R/traceMem: wired.mem=1.593405 GiB
2025-09-23 11:17:03.388834 DEBUG::tools.R/traceMem: wired.mem=8.075457 GiB
2025-09-23 11:18:03.464903 DEBUG::tools.R/traceMem: wired.mem=1.810772 GiB
2025-09-23 11:19:03.540877 DEBUG::tools.R/traceMem: wired.mem=7.406989 GiB
2025-09-23 11:20:03.605744 DEBUG::tools.R/traceMem: wired.mem=-1.140920 GiB
2025-09-23 11:21:03.684851 DEBUG::tools.R/traceMem: wired.mem=-3.055940 GiB
2025-09-23 11:22:03.760839 DEBUG::tools.R/traceMem: wired.mem=3.458060 GiB
2025-09-23 11:23:03.83686 DEBUG::tools.R/traceMem: wired.mem=1.101771 GiB
2025-09-23 11:24:03.912968 DEBUG::tools.R/traceMem: wired.mem=5.415080 GiB
2025-09-23 11:25:03.988965 DEBUG::tools.R/traceMem: wired.mem=2.996384 GiB
2025-09-23 11:26:04.064871 DEBUG::tools.R/traceMem: wired.mem=-2.727432 GiB
2025-09-23 11:27:04.140895 DEBUG::tools.R/traceMem: wired.mem=-2.533118 GiB
2025-09-23 11:28:04.208843 DEBUG::tools.R/traceMem: wired.mem=-4.004352 GiB
2025-09-23 11:29:04.284894 DEBUG::tools.R/traceMem: wired.mem=-5.723951 GiB
2025-09-23 11:30:04.35873 DEBUG::tools.R/traceMem: wired.mem=1.235579 GiB
2025-09-23 11:31:04.432827 DEBUG::tools.R/traceMem: wired.mem=-8.523928 GiB
2025-09-23 11:32:04.504937 DEBUG::tools.R/traceMem: wired.mem=-7.861858 GiB
2025-09-23 11:33:04.569427 DEBUG::tools.R/traceMem: wired.mem=-5.107519 GiB

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

nameusersystemelapsed
HTSeqGenie000
buildGenomicFeaturesFromTxDb000
runPipeline000